Merge branch 'patch-flexiprep' into 'develop'

Patch flexiprep

found bug in flexiprep, seqstat can't find fastq when input fastq (extracted by zcat) is removed because only input is the link file from seqtk.

Is this hot fix worthy? I not sure but it could be a blocking bug.

See merge request !136

public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala

@@ -166,14 +166,16 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
 
     var R1: File = new File(R1_in)
     var R2: File = if (paired) new File(R2_in) else null
-    var deps: List[File] = if (paired) List(R1, R2) else List(R1)
+    var deps_R1: List[File] = R1 :: Nil
+    var deps_R2: List[File] = if (paired) R2 :: Nil else Nil
+    def deps: List[File] = deps_R1 ::: deps_R2
 
     val seqtkSeq_R1 = SeqtkSeq(this, R1, swapExt(outDir, R1, R1_ext, ".sanger" + R1_ext), fastqc_R1)
     seqtkSeq_R1.isIntermediate = true
     add(seqtkSeq_R1)
     addSummarizable(seqtkSeq_R1, "seqtkSeq_R1")
     R1 = seqtkSeq_R1.output
-    deps ::= R1
+    deps_R1 ::= R1
 
     if (paired) {
       val seqtkSeq_R2 = SeqtkSeq(this, R2, swapExt(outDir, R2, R2_ext, ".sanger" + R2_ext), fastqc_R2)
@@ -181,17 +183,19 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
       add(seqtkSeq_R2)
       addSummarizable(seqtkSeq_R2, "seqtkSeq_R2")
       R2 = seqtkSeq_R2.output
-      deps ::= R2
+      deps_R2 ::= R2
     }
 
     val seqstat_R1 = Seqstat(this, R1, outDir)
     seqstat_R1.isIntermediate = true
+    seqstat_R1.deps = deps_R1
     add(seqstat_R1)
     addSummarizable(seqstat_R1, "seqstat_R1")
 
     if (paired) {
       val seqstat_R2 = Seqstat(this, R2, outDir)
       seqstat_R2.isIntermediate = true
+      seqstat_R2.deps = deps_R2
       add(seqstat_R2)
       addSummarizable(seqstat_R2, "seqstat_R2")
     }
@@ -201,10 +205,11 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
       val cutadapt_R1 = Cutadapt(this, R1, swapExt(outDir, R1, R1_ext, ".clip" + R1_ext))
       cutadapt_R1.fastqc = fastqc_R1
       cutadapt_R1.isIntermediate = true
+      cutadapt_R1.deps = deps_R1
       add(cutadapt_R1)
       addSummarizable(cutadapt_R1, "clipping_R1")
       R1 = cutadapt_R1.fastq_output
-      deps ::= R1
+      deps_R1 ::= R1
       outputFiles += ("cutadapt_R1_stats" -> cutadapt_R1.stats_output)
 
       if (paired) {
@@ -212,10 +217,11 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
         outputFiles += ("cutadapt_R2_stats" -> cutadapt_R2.stats_output)
         cutadapt_R2.fastqc = fastqc_R2
         cutadapt_R2.isIntermediate = true
+        cutadapt_R2.deps = deps_R2
         add(cutadapt_R2)
         addSummarizable(cutadapt_R2, "clipping_R2")
         R2 = cutadapt_R2.fastq_output
-        deps ::= R2
+        deps_R2 ::= R2
 
         val fqSync = new FastqSync(this)
         fqSync.refFastq = cutadapt_R1.fastq_input
@@ -230,7 +236,8 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
         outputFiles += ("syncStats" -> fqSync.outputStats)
         R1 = fqSync.outputFastq1
         R2 = fqSync.outputFastq2
-        deps :::= R1 :: R2 :: Nil
+        deps_R1 ::= R1
+        deps_R2 ::= R2
       }
     }
 
@@ -253,13 +260,13 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
     }
 
     val seqstat_R1_after = Seqstat(this, R1, outDir)
-    seqstat_R1_after.deps = deps
+    seqstat_R1_after.deps = deps_R1
     add(seqstat_R1_after)
     addSummarizable(seqstat_R1_after, "seqstat_R1_after")
 
     if (paired) {
       val seqstat_R2_after = Seqstat(this, R2, outDir)
-      seqstat_R2_after.deps = deps
+      seqstat_R2_after.deps = deps_R2
       add(seqstat_R2_after)
       addSummarizable(seqstat_R2_after, "seqstat_R2_after")
     }